Merge branch 'release' - publish for v1.2.1

Author: yingzhanguri

NEWS.md

@@ -1,3 +1,8 @@
+v1.2.1 (2022-05-12)
+------------------
+- fix bug in `generate-database`
+- revise formatting of doc
+
 v1.2 (2022-05-10)
 ------------------
 

docs/tutorial/generating_models.rst

@@ -47,7 +47,7 @@ organism of interest within the class Mollicutes.
 
 
 Basic use of the ``generate-database`` command
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+----------------------------------------------
 
 As noted above, the `generate-database` command uses an annotation file to
 query the KEGG database and download reaction data. You will need an
@@ -129,7 +129,7 @@ column in the table specified with `--annotations`
 
 
 Basic use of the ``generate-transporters`` command
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+--------------------------------------------------
 
 In addition to the database of metabolic reactions, another important
 component of metabolic models is the presence of transporters. These

psamm/generate_model.py

@@ -921,8 +921,7 @@ def init_parser(cls, parser):
     def run(self):
         """Entry point for the database generation script"""
         # check if required packages are installed
-        if 'Bio.KEGG.Enzyme' not in sys.modules or \
-                'Bio.KEGG.REST' not in sys.modules:
+        if 'Bio.KEGG.REST' not in sys.modules:
             quit('No biopython package found. '
                  'Please run <pip install biopython>''')
         if "libchebipy._chebi_entity" not in sys.modules:

setup.py

@@ -51,7 +51,7 @@
 
 setup(
     name='psamm',
-    version='1.2',
+    version='1.2.1',
     description='PSAMM metabolic modeling tools',
     maintainer='Jon Lund Steffensen',
     maintainer_email='jon_steffensen@uri.edu',